Release Date: Unreleased
Development Changelog: dev
New output_path = ":cache:" to store downloaded reference files in a
dedicated cache folder.
This is the new default behavior for download_reference().
New get_isoformic_cache() function to retrieve the path to the cache folder.
New IsoformicExperiment class to encapsulate all workflow inputs with a
disk-based backend and tidy interface.
New generics and methods for the IsoformicExperiment class:
col_data() - Retrieve Sample Metadata
row_data() - Retrieve Metadata for Transcripts in the Assay Data
annot_data() - Retrieve Aggregated Annotation Data (transcript-centric)
annot_data_transcripts() - Retrieve Transcript Annotation Data
annot_data_genes() - Retrieve Gene Annotation Data
annot_data_exons() - Retrieve Exon Annotation Data
tx_to_gene() - Retrieve Transcript to Gene Mapping from the Annotation
summarize_to_gene() - Summarize Transcript-level Expression to Gene-level
de_tx() - Retrieve Differential Expression Results for Transcripts
de_gene() - Retrieve Differential Expression Results for Genes
New interface for plot_log2fc() function to visualize log2 fold changes of
transcripts within a gene.
New feature_column argument in plot_log2FC() to specify the column
name in the DE results table that contains the feature names (e.g., gene or
transcript names).
New file_type = "genome_fasta" option in download_reference() to
download the genome FASTA file from GENCODE.
file_type in download_reference() is now "gff" by default.version in download_reference() is now "49" by default.output_path in download_reference() is now ":cache:".DEG_DET_table and selected_genes in plot_log2FC() are now
de_data and feature.Release Date: 2025-10-06
Development Changelog: 0.1.2
parse_annotation().plot_genomic_context() function to visualize the genomic context of a
gene with its transcripts.tx_type_palette() function to provide a default color palette for
transcript types.make_tx_to_gene() output, wrong column name entrez_id replaced for tx_length.Release Date: 2024-06-18
Development Changelog: 0.1.1
download_reference(): now supports organism = c("human", "mouse"),
with organism = "human" being the default.download_reference(): argument file_type = "gtf" is the default.prepare_annotation(): Parse both GTF and GFF file formats into
required annotation data.prepare_profile_data(): accepts matrix and data.frame as input for the txi_transcript argument.Release Date: 2024-06-11
Development Changelog: 0.1.0
Release Date: 2024-06-08
Development Changelog: 0.0.1